WASHINGTON — American intelligence agencies have concluded with “high confidence” that Russia acted covertly in the latter stages of the presidential campaign to harm Hillary Clinton’s chances and promote Donald J. Trump, according to senior administration officials.

They based that conclusion, in part, on another finding — which they say was also reached with high confidence — that the Russians hacked the Republican National Committee’s computer systems in addition to their attacks on Democratic organizations, but did not release whatever information they gleaned from the Republican networks.

In the months before the election, it was largely documents from Democratic Party systems that were leaked to the public. Intelligence agencies have concluded that the Russians gave the Democrats’ documents to WikiLeaks.

Republicans have a different explanation for why no documents from their networks were ever released. Over the past several months, officials from the Republican committee have consistently said that their networks were not compromised, asserting that only the accounts of individual Republicans were attacked. On Friday, a senior committee official said he had no comment.

Mr. Trump’s transition office issued a statement Friday evening reflecting the deep divisions that emerged between his campaign and the intelligence agencies over Russian meddling in the election. “These are the same people that said Saddam Hussein had weapons of mass destruction,” the statement said. “The election ended a long time ago in one of the biggest Electoral College victories in history. It’s now time to move on and ‘Make America Great Again.’”

One senior government official, who had been briefed on an F.B.I. investigation into the matter, said that while there were attempts to penetrate the Republican committee’s systems, they were not successful.

But the intelligence agencies’ conclusions that the hacking efforts were successful, which have been presented to President Obama and other senior officials, add a complex wrinkle to the question of what the Kremlin’s evolving objectives were in intervening in the American presidential election.

“We now have high confidence that they hacked the D.N.C. and the R.N.C., and conspicuously released no documents” from the Republican organization, one senior administration official said, referring to the Russians.

It is unclear how many files were stolen from the Republican committee; in some cases, investigators never get a clear picture. It is also far from clear that Russia’s original intent was to support Mr. Trump, and many intelligence officials — and former officials in Mrs. Clinton’s campaign — believe that the primary motive of the Russians was to simply disrupt the campaign and undercut confidence in the integrity of the vote.

The Russians were as surprised as everyone else at Mr. Trump’s victory, intelligence officials said. Had Mrs. Clinton won, they believe, emails stolen from the Democratic committee and from senior members of her campaign could have been used to undercut her legitimacy. The intelligence agencies’ conclusion that Russia tried to help Mr. Trump was first reported by The Washington Post.

In briefings to the White House and Congress, intelligence officials, including those from the C.I.A. and the National Security Agency, have identified individual Russian officials they believe were responsible. But none have been publicly penalized.

It is possible that in hacking into the Republican committee, Russian agents were simply hedging their bets. The attack took place in the spring, the senior officials said, about the same time that a group of hackers believed to be linked to the G.R.U., Russia’s military intelligence agency, stole the emails of senior officials of the Democratic National Committee. Intelligence agencies believe that the Republican committee hack was carried out by the same Russians who penetrated the Democratic committee and other Democratic groups.

The finding about the Republican committee is expected to be included in a detailed report of “lessons learned” that Mr. Obama has ordered intelligence agencies to assemble before he leaves office on Jan. 20. That report is intended, in part, to create a comprehensive history of the Russian effort to influence the election, and to solidify the intelligence findings before Mr. Trump is sworn in.

Mr. Trump has repeatedly cast doubt about any intelligence suggesting a Russian effort to influence the election. “I don’t believe they interfered,” he told Time magazine in an interview published this week. He suggested that hackers could come from China, or that “it could be some guy in his home in New Jersey.”

Intelligence officials and private cybersecurity companies believe that the Democratic National Committee was hacked by two different Russian cyberunits. One, called “Cozy Bear” or “A.P.T. 29” by some Western security experts, is believed to have spent months inside the D.N.C. computer network, as well as other government and political institutions, but never made public any of the documents it took. (A.P.T. stands for “Advanced Persistent Threat,” which usually describes a sophisticated state-sponsored cyberintruder.)

The other, the G.R.U.-controlled unit known as “Fancy Bear,” or “A.P.T. 28,” is believed to have created two outlets on the internet, Guccifer 2.0 and DCLeaks, to make Democratic documents public. Many of the documents were also provided to WikiLeaks, which released them over many weeks before the Nov. 8 election.

Representative Michael McCaul, the Texas Republican who is the chairman of the House Homeland Security Committee, said on CNN in September that the R.N.C. had been hacked by Russia, but then quickly withdrew the claim.

Mr. McCaul, who was considered by Mr. Trump for secretary of Homeland Security, initially told CNN’s Wolf Blitzer, “It’s important to note, Wolf, that they have not only hacked into the D.N.C. but also into the R.N.C.” He added that “the Russians have basically hacked into both parties at the national level, and that gives us all concern about what their motivations are.”

Minutes later, the R.N.C. issued a statement denying that it had been hacked. Mr. McCaul subsequently said that he had misspoken, but that it was true that “Republican political operatives” had been the target of Russian hacking. So were establishment Republicans with no ties to the campaign, including former Secretary of State Colin L. Powell.

Mr. McCaul may have had in mind a collection of more than 200 emails of Republican officials and activists that appeared this year on the website DCLeaks.com. That website got far more attention for the many Democratic Party documents it posted.

The messages stolen from Republicans have drawn little attention because most are routine business emails from local Republican Party officials in several states, congressional staff members and party activists.

Among those whose emails were posted was Peter W. Smith, who runs a venture capital firm in Chicago and has long been active in “opposition research” for the Republican Party. He said he was unaware that his emails had been hacked until he was called by a reporter on Thursday.

He said he believes that his material came from a hack of the Illinois Republican Party.

“I’m not upset at all,” he said. “I try in my communications, quite frankly, not to say anything that would be embarrassing if made public.”